Filter by attribute:
Check the boxes below to include SNPs with those attributes. In order to be displayed, a SNP must pass the filter for each category.
Some assemblies may not contain any SNPs that have some of the listed attributes.

The selected "Feature for Color Specification" above has the
selection of colors below for each attribute. Only the color
options for the feature selected above will be used to color items;
color options for other features will not be shown.
If a SNP has more than one of these attributes, the stronger color will override the
weaker color. The order of colors, from strongest to weakest, is red,
green, blue, gray, and black.

Description

This track contains information about a subset of the
single nucleotide polymorphisms
and small insertions and deletions (indels) — collectively Simple
Nucleotide Polymorphisms — from
dbSNP
build 151, available from
ftp.ncbi.nlm.nih.gov/snp.
Only SNPs flagged as clinically associated by dbSNP,
mapped to a single location in the reference genome assembly, and
not known to have a minor allele frequency of at
least 1%, are included in this subset.
Frequency data are not available for all SNPs, so this subset probably
includes some SNPs whose true minor allele frequency is 1% or greater.

The significance of any particular variant in this track should be
interpreted only by a trained medical geneticist using all available
information. For example, some variants are included in this track
because of their inclusion in a Locus-Specific Database (LSDB) or
mention in OMIM, but are not thought to be disease-causing, so
inclusion of a variant in this track is not necessarily an indicator
of risk. Again, all available information must be carefully considered
by a qualified professional.

Mult. SNPs(151) - SNPs mapping in more than one place on reference assembly.

All SNPs(151) - all SNPs from dbSNP mapping to reference assembly.

Interpreting and Configuring the Graphical Display

Variants are shown as single tick marks at most zoom levels.
When viewing the track at or near base-level resolution, the displayed
width of the SNP corresponds to the width of the variant in the reference
sequence. Insertions are indicated by a single tick mark displayed between
two nucleotides, single nucleotide polymorphisms are displayed as the width
of a single base, and multiple nucleotide variants are represented by a
block that spans two or more bases.

On the track controls page, SNPs can be colored and/or filtered from the
display according to several attributes:

Class: Describes the observed alleles

Single - single nucleotide variation: all observed alleles are single nucleotides
(can have 2, 3 or 4 alleles)

Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,
both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),
not shown in UCSC Genome Browser.
A variant may have more than one functional role if it overlaps
multiple transcripts.
These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the
MISO Sequence Ontology Browser.

Unknown - no functional classification provided (possibly intergenic)

synonymous_variant -
A sequence variant where there is no resulting change to the encoded amino acid
(dbSNP term: coding-synon)

stop_gained -
A sequence variant whereby at least one base of a codon is changed, resulting in
a premature stop codon, leading to a shortened transcript
(dbSNP term: nonsense)

missense_variant -
A sequence variant, where the change may be longer than 3 bases, and at least
one base of a codon is changed resulting in a codon that encodes for a
different amino acid
(dbSNP term: missense)

stop_lost -
A sequence variant where at least one base of the terminator codon (stop)
is changed, resulting in an elongated transcript
(dbSNP term: stop-loss)

frameshift_variant -
A sequence variant which causes a disruption of the translational reading frame,
because the number of nucleotides inserted or deleted is not a multiple of three
(dbSNP term: frameshift)

inframe_indel -
A coding sequence variant where the change does not alter the frame
of the transcript
(dbSNP term: cds-indel)

splice_acceptor_variant -
A splice variant that changes the 2 base region at the 3' end of an intron
(dbSNP term: splice-3)

splice_donor_variant -
A splice variant that changes the 2 base region at the 5' end of an intron
(dbSNP term: splice-5)

In the Coloring Options section of the track controls page,
function terms are grouped into several categories, shown here with default colors.
If a SNP has more than one of these attributes, the stronger color will override
the weaker color. The order of colors, from strongest to weakest, is red, green,
blue, gray, and black.

DuplicateObserved,
MixedObserved - Multiple distinct insertion SNPs have
been mapped to this location, with either the same inserted
sequence (Duplicate) or different inserted sequence (Mixed).

FlankMismatchGenomeEqual,
FlankMismatchGenomeLonger,
FlankMismatchGenomeShorter - NCBI's alignment of
the flanking sequences had at least one mismatch or gap
near the mapped SNP position.
(UCSC's re-alignment of flanking sequences to the genome may
be informative.)

MultipleAlignments - This SNP's flanking sequences
align to more than one location in the reference assembly.

NamedDeletionZeroSpan - A deletion (from the
genome) was observed but the annotation spans 0 bases.
(UCSC's re-alignment of flanking sequences to the genome may
be informative.)

NamedInsertionNonzeroSpan - An insertion (into the
genome) was observed but the annotation spans more than 0
bases. (UCSC's re-alignment of flanking sequences to the
genome may be informative.)

NonIntegerChromCount - At least one allele
frequency corresponds to a non-integer (+-0.010000) count of
chromosomes on which the allele was observed. The reported
total sample count for this SNP is probably incorrect.

Clinically Associated (human only) - SNP is in OMIM and/or at
least one submitter is a Locus-Specific Database. This does
not necessarily imply that the variant causes any disease,
only that it has been observed in clinical studies.

Has Microattribution/Third-Party Annotation - At least
one of the SNP's submitters studied this SNP in a biomedical
setting, but is not a Locus-Specific Database or OMIM/OMIA.

Submitted by Locus-Specific Database - At least one of
the SNP's submitters is associated with a database of variants
associated with a particular gene. These variants may or may
not be known to be causative.

MAF >= 5% in Some Population - Minor Allele Frequency is
at least 5% in at least one population assayed.

MAF >= 5% in All Populations - Minor Allele Frequency is
at least 5% in all populations assayed.

Genotype Conflict - Quality check: different genotypes
have been submitted for the same individual.

Average heterozygosity should not exceed 0.5 for bi-allelic
single-base substitutions.

Weight: Alignment quality assigned by dbSNP. Before dbSNP build
147, weight had values 1, 2 or 3, with 1 being the highest quality
(mapped to a single genomic location). As of dbSNP build 147, dbSNP
now releases only the variants with weight 1.

Submitter handles: These are short, single-word identifiers of
labs or consortia that submitted SNPs that were clustered into this
reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs
have been observed by many different submitters, and some by only a
single submitter (although that single submitter may have tested a
large number of samples).

AlleleFrequencies: Some submissions to dbSNP include
allele frequencies and the study's sample size
(i.e., the number of distinct chromosomes, which is two times the
number of individuals assayed, a.k.a. 2N). dbSNP combines all
available frequencies and counts from submitted SNPs that are
clustered together into a reference SNP.

You can configure this track such that the details page displays
the function and coding differences relative to
particular gene sets. Choose the gene sets from the list on the SNP
configuration page displayed beneath this heading: On details page,
show function and coding differences relative to.
When one or more gene tracks are selected, the SNP details page
lists all genes that the SNP hits (or is close to), with the same keywords
used in the function category. The function usually
agrees with NCBI's function, except when NCBI's functional annotation is
relative to an XM_* predicted RefSeq (not included in the UCSC Genome
Browser's RefSeq Genes track) and/or UCSC's functional annotation is
relative to a transcript that is not in RefSeq.

Insertions/Deletions

dbSNP uses a class called 'in-del'. We compare the length of the
reference allele to the length(s) of observed alleles; if the
reference allele is shorter than all other observed alleles, we change
'in-del' to 'insertion'. Likewise, if the reference allele is longer
than all other observed alleles, we change 'in-del' to 'deletion'.

UCSC Re-alignment of flanking sequences

dbSNP determines the genomic locations of SNPs by aligning their flanking
sequences to the genome.
UCSC displays SNPs in the locations determined by dbSNP, but does not
have access to the alignments on which dbSNP based its mappings.
Instead, UCSC re-aligns the flanking sequences
to the neighboring genomic sequence for display on SNP details pages.
While the recomputed alignments may differ from dbSNP's alignments,
they often are informative when UCSC has annotated an unusual condition.

Non-repetitive genomic sequence is shown in upper case like the flanking
sequence, and a "|" indicates each match between genomic and flanking bases.
Repetitive genomic sequence (annotated by RepeatMasker and/or the
Tandem Repeats Finder with period >= 12) is shown in lower case, and matching
bases are indicated by a "+".

Functional classification was obtained from
b151_SNPContigLocusId_N.bcp.gz. The internal database representation
uses dbSNP's function terms, but for display in SNP details pages,
these are translated into
Sequence Ontology terms.

Validation status and heterozygosity were obtained from SNP.bcp.gz.

SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.
For the human assembly, allele frequencies were also taken from
SNPAlleleFreq_TGP.bcp.gz .

Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and
SNPSubSNPLink.bcp.gz.

SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,
such as clinically-associated. See the document
dbSNP_BitField_v5.pdf for details.

The header lines in the rs_fasta files were used for molecule type,
class and observed polymorphism.

Orthologous Alleles (human assemblies only)

For the human assembly, we provide a related table that contains
orthologous alleles in the chimpanzee, orangutan and rhesus macaque
reference genome assemblies.
We use our liftOver utility to identify the orthologous alleles.
The candidate human SNPs are a filtered list that meet the criteria:

class = 'single'

mapped position in the human reference genome is one base long

aligned to only one location in the human reference genome

not aligned to a chrN_random chrom

biallelic (not tri- or quad-allelic)

In some cases the orthologous allele is unknown; these are set to 'N'.
If a lift was not possible, we set the orthologous allele to '?' and the
orthologous start and end position to 0 (zero).

Masked FASTA Files (human assemblies only)

FASTA files that have been modified to use
IUPAC
ambiguous nucleotide characters at
each base covered by a single-base substitution are available for download:
GRCh37/hg19, GRCh38/hg38.
Note that only single-base substitutions (no insertions or deletions) were used
to mask the sequence, and these were filtered to exclude problematic SNPs.